CLI

Command Line Interface¶

Our package features a Python command-line interface (CLI) script called "dcTMD".

The script loads the constraint force files, generates a work/force set, and calculates the mean work, dissipated work, free energy, and friction factor. The output is saved as a .npz and .dat file, and the work/force set can be saved separately using the "--save_dataset" option. Furthermore, with the --plot option an overview plot of the results in generated.

The CLI also provides a verbose mode for debugging and error reporting.

To get an overview over all modules simply run the following command in the shell.

In [4]:

%%bash
python -m dcTMD

%%bash python -m dcTMD

Usage: python -m dcTMD [OPTIONS]

  ------------------------- |         dcTMD         |
  ------------------------- Calculate free energy and friction for given
  constraint force files.

  Analysis tools for dissipation-corrected targeted molecular dynamics, which
  is an enhanced sampling method to enforce rare events in biomolecular
  systems. When publishing results gained with this python package, please
  cite the following publications: (1) Tänzel, Victor and Jäger, Miriam and
  Wolf, Steffen in preparation. (2) Wolf, Steffen, and Gerhard Stock.
  "Targeted molecular dynamics calculations of free energy profiles using a
  nonequilibrium friction correction." Journal of chemical theory and
  computation 14.12 (2018): 6175- 6182.

Options:
  -m, --mode [work|force]  Use either work or force autocovariance function to
                           calculatedcTMD quantities.  [default: work;
                           required]
  -f, --file TEXT          Input: File containing list of all constraint force
                           file namesor glob pattern e.g."*.xvg" to generate a
                           list of all constraint force files using
                           glob.glob()  [required]
  -o, --outname PATH       Output: Path/prefix of output names.
  -T, --temperature FLOAT  Simulation temperature in K.  [required]
  -vel, --velocity FLOAT   Pulling velocity in nm/ps.  [required]
  --res INTEGER            Striding to reduce size of returned free energy and
                           friction  [default: 1]
  -s, --sigma FLOAT        Standard deviation of gaussian filter in nm.
  --resamples INTEGER      Number of resamples used in optional bootstrapping.
                           This is only available in mode work
  -v, --verbose            Enable verbose mode.  [default: False]
  -p, --plot               Plots free energy and smoothed friction.  [default:
                           False]
  -sd, --save_dataset      Save the Work/ForceSet class to file.  [default:
                           False]
  --help                   Show this message and exit.

In [ ]:

# Usage example:
python -m dcTMD -f '*.xvg' -o path/to/output/name  -T 290.5 -v 0.001 --verbose --plot --save_dataset

# Usage example: python -m dcTMD -f '*.xvg' -o path/to/output/name -T 290.5 -v 0.001 --verbose --plot --save_dataset